Input tree (Ti)

This mode allows the user to input a species tree. In this case, the command is slightly different:

python3 Zombi.py Ti YourTreeFileInNewick ./Output_folder

This command will translate your tree into a file with the events taken place on it, something used by the other modes of Zombi. If you want to simulate genomes in your own tree, running this command is a prerequisite.

Watch out! Your tree must be ultrametric, otherwise, Zombi has no way to know which species survive till the present time